Starting phenix.real_space_refine on Thu Mar 21 17:17:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvq_34136/03_2024/7yvq_34136.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvq_34136/03_2024/7yvq_34136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvq_34136/03_2024/7yvq_34136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvq_34136/03_2024/7yvq_34136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvq_34136/03_2024/7yvq_34136.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvq_34136/03_2024/7yvq_34136.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 47 5.16 5 C 19238 2.51 5 N 5003 2.21 5 O 6433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30742 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "B" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "C" Number of atoms: 3867 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Chain: "D" Number of atoms: 3898 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 497, 3898 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 477} Chain breaks: 1 Chain: "E" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 493, 3857 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain breaks: 2 bond proxies already assigned to first conformer: 3852 Chain: "F" Number of atoms: 3867 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Chain: "G" Number of atoms: 3935 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3867 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 464} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 3776 Chain: "H" Number of atoms: 3349 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 413, 3346 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 390} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 413, 3346 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 390} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 3414 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 77 residue: pdb=" N AGLY A 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 488 " occ=0.50 residue: pdb=" N ATHR A 489 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 489 " occ=0.50 residue: pdb=" N ALYS A 490 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 490 " occ=0.50 residue: pdb=" N AASN A 491 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 491 " occ=0.50 residue: pdb=" N ASER A 492 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 492 " occ=0.50 residue: pdb=" N ASER A 493 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 493 " occ=0.50 residue: pdb=" N AGLY A 494 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 494 " occ=0.50 residue: pdb=" N AGLN A 495 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 495 " occ=0.50 residue: pdb=" N AILE A 496 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 496 " occ=0.50 residue: pdb=" N AVAL A 497 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 497 " occ=0.50 residue: pdb=" N THR A 498 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THR A 498 " occ=0.50 residue: pdb=" N AGLY B 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 488 " occ=0.50 ... (remaining 65 not shown) Time building chain proxies: 23.60, per 1000 atoms: 0.77 Number of scatterers: 30742 At special positions: 0 Unit cell: (189.2, 176.88, 177.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 47 16.00 O 6433 8.00 N 5003 7.00 C 19238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.35 Conformation dependent library (CDL) restraints added in 9.0 seconds 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7338 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 61 sheets defined 20.3% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.665A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.925A pdb=" N ASP A 291 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.850A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.607A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 594 removed outlier: 3.631A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.773A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.973A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.645A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 593 Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.950A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.957A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.934A pdb=" N ILE C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.877A pdb=" N ASP C 505 " --> pdb=" O SER C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.621A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 595 removed outlier: 3.779A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.848A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.807A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 502 through 505 removed outlier: 3.728A pdb=" N ASP D 505 " --> pdb=" O SER D 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 502 through 505' Processing helix chain 'D' and resid 506 through 513 removed outlier: 3.554A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.726A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.834A pdb=" N GLU E 251 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 290 removed outlier: 3.517A pdb=" N ARG E 290 " --> pdb=" O THR E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.023A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 503 through 513 removed outlier: 4.549A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 595 removed outlier: 4.033A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.582A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU F 251 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.934A pdb=" N ILE F 429 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 503 through 512 removed outlier: 3.527A pdb=" N ILE F 507 " --> pdb=" O TRP F 503 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 572 through 576 removed outlier: 3.876A pdb=" N VAL F 576 " --> pdb=" O GLU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 593 removed outlier: 3.852A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.559A pdb=" N ALA G 250 " --> pdb=" O ASP G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.943A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.039A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.674A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.938A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'H' and resid 13 through 31 removed outlier: 3.816A pdb=" N TRP H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS H 30 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 60 through 67 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.925A pdb=" N ASN H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 115 through 127 Processing helix chain 'H' and resid 217 through 229 removed outlier: 3.967A pdb=" N ALA H 226 " --> pdb=" O SER H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 235 removed outlier: 3.897A pdb=" N LYS H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU H 235 " --> pdb=" O TRP H 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 230 through 235' Processing helix chain 'H' and resid 236 through 248 removed outlier: 3.814A pdb=" N MET H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 260 removed outlier: 4.478A pdb=" N ALA H 253 " --> pdb=" O GLY H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 removed outlier: 3.591A pdb=" N ASN H 265 " --> pdb=" O ASN H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 283 Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.556A pdb=" N PHE H 349 " --> pdb=" O MET H 346 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA H 350 " --> pdb=" O SER H 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 346 through 350' Processing helix chain 'H' and resid 370 through 372 No H-bonds generated for 'chain 'H' and resid 370 through 372' Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 311 removed outlier: 5.739A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 330 removed outlier: 3.550A pdb=" N SER A 316 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER A 374 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 328 " --> pdb=" O ALA A 366 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 365 through 382 current: chain 'B' and resid 365 through 370 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 365 through 370 current: chain 'C' and resid 365 through 382 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 365 through 382 current: chain 'D' and resid 365 through 382 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 365 through 382 current: chain 'E' and resid 365 through 376 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 365 through 376 current: chain 'F' and resid 365 through 382 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 365 through 382 current: chain 'G' and resid 366 through 382 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 423 removed outlier: 7.011A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.232A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA8, first strand: chain 'A' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 618 through 620 current: chain 'A' and resid 705 through 706 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.540A pdb=" N ILE A 656 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 723 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 722 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 689 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB2, first strand: chain 'B' and resid 300 through 311 removed outlier: 6.885A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 403 through 413 removed outlier: 4.982A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.302A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AB7, first strand: chain 'B' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 618 through 620 current: chain 'B' and resid 705 through 706 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.542A pdb=" N GLU B 722 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 724 " --> pdb=" O LYS B 687 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 687 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 684 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 698 " --> pdb=" O ILE B 684 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 694 " --> pdb=" O ILE B 688 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 311 removed outlier: 6.828A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 418 through 423 removed outlier: 7.027A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AC4, first strand: chain 'C' and resid 526 through 531 removed outlier: 9.323A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AC6, first strand: chain 'C' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 618 through 620 current: chain 'C' and resid 705 through 706 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 693 through 698 removed outlier: 3.974A pdb=" N LYS C 694 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 698 " --> pdb=" O ILE C 684 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AC9, first strand: chain 'D' and resid 300 through 311 removed outlier: 5.802A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.919A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 526 through 531 removed outlier: 9.174A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AD5, first strand: chain 'D' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 618 through 620 current: chain 'D' and resid 705 through 706 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 655 through 658 removed outlier: 3.979A pdb=" N ILE D 656 " --> pdb=" O ILE D 723 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 723 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU D 722 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 689 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D 688 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 694 " --> pdb=" O ILE D 688 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AD8, first strand: chain 'E' and resid 300 through 311 removed outlier: 6.921A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 403 through 413 removed outlier: 4.841A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AE2, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.125A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AE4, first strand: chain 'E' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 618 through 620 current: chain 'E' and resid 705 through 706 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 694 through 698 removed outlier: 3.548A pdb=" N LYS E 694 " --> pdb=" O ILE E 688 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU E 722 " --> pdb=" O LYS E 689 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AE7, first strand: chain 'F' and resid 300 through 311 removed outlier: 5.749A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 403 through 413 removed outlier: 4.949A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 524 through 531 removed outlier: 3.741A pdb=" N GLU F 524 " --> pdb=" O THR F 521 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AF2, first strand: chain 'F' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 618 through 620 current: chain 'F' and resid 705 through 706 No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 655 through 658 removed outlier: 3.896A pdb=" N ILE F 656 " --> pdb=" O ILE F 723 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE F 723 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 721 " --> pdb=" O ILE F 658 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU F 722 " --> pdb=" O LYS F 689 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AF5, first strand: chain 'G' and resid 300 through 311 removed outlier: 6.803A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.790A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS G 405 " --> pdb=" O AGLY G 485 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N AGLY G 485 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR G 407 " --> pdb=" O AVAL G 483 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N AVAL G 483 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR G 409 " --> pdb=" O ATHR G 481 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AF8, first strand: chain 'G' and resid 525 through 531 removed outlier: 9.456A pdb=" N ILE G 611 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AG1, first strand: chain 'G' and resid 618 through 620 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 618 through 620 current: chain 'G' and resid 705 through 706 No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'G' and resid 655 through 658 removed outlier: 3.970A pdb=" N ILE G 688 " --> pdb=" O LYS G 694 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS G 694 " --> pdb=" O ILE G 688 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 684 through 685 Processing sheet with id=AG4, first strand: chain 'H' and resid 89 through 94 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 89 through 94 current: chain 'H' and resid 175 through 195 removed outlier: 6.731A pdb=" N GLU H 204 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE H 190 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS H 202 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG H 192 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR H 200 " --> pdb=" O ARG H 192 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL H 194 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 291 through 297 removed outlier: 6.470A pdb=" N VAL H 355 " --> pdb=" O VAL H 407 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 330 through 333 Processing sheet with id=AG7, first strand: chain 'H' and resid 337 through 340 removed outlier: 3.906A pdb=" N ILE H 337 " --> pdb=" O LEU H 383 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 1766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.08 Time building geometry restraints manager: 12.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.34: 9970 1.34 - 1.49: 8065 1.49 - 1.65: 13138 1.65 - 1.81: 87 Bond restraints: 31261 Sorted by residual: bond pdb=" CG PRO D 629 " pdb=" CD PRO D 629 " ideal model delta sigma weight residual 1.503 1.020 0.483 3.40e-02 8.65e+02 2.02e+02 bond pdb=" N PRO D 629 " pdb=" CD PRO D 629 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" N GLN C 644 " pdb=" CA GLN C 644 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.01e+01 bond pdb=" N ASP E 717 " pdb=" CA ASP E 717 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.10e-02 8.26e+03 9.17e+00 bond pdb=" CA ASP E 717 " pdb=" C ASP E 717 " ideal model delta sigma weight residual 1.521 1.556 -0.034 1.14e-02 7.69e+03 9.10e+00 ... (remaining 31256 not shown) Histogram of bond angle deviations from ideal: 76.02 - 87.76: 2 87.76 - 99.51: 3 99.51 - 111.25: 13139 111.25 - 123.00: 26221 123.00 - 134.75: 2999 Bond angle restraints: 42364 Sorted by residual: angle pdb=" N PRO D 629 " pdb=" CD PRO D 629 " pdb=" CG PRO D 629 " ideal model delta sigma weight residual 103.20 76.02 27.18 1.50e+00 4.44e-01 3.28e+02 angle pdb=" CA PRO D 629 " pdb=" CB PRO D 629 " pdb=" CG PRO D 629 " ideal model delta sigma weight residual 104.50 84.49 20.01 1.90e+00 2.77e-01 1.11e+02 angle pdb=" CA PRO D 629 " pdb=" N PRO D 629 " pdb=" CD PRO D 629 " ideal model delta sigma weight residual 112.00 100.79 11.21 1.40e+00 5.10e-01 6.41e+01 angle pdb=" N ASN C 720 " pdb=" CA ASN C 720 " pdb=" C ASN C 720 " ideal model delta sigma weight residual 107.32 119.20 -11.88 1.65e+00 3.67e-01 5.19e+01 angle pdb=" CA PHE F 281 " pdb=" CB PHE F 281 " pdb=" CG PHE F 281 " ideal model delta sigma weight residual 113.80 119.85 -6.05 1.00e+00 1.00e+00 3.66e+01 ... (remaining 42359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17311 17.96 - 35.93: 1382 35.93 - 53.89: 273 53.89 - 71.86: 67 71.86 - 89.82: 31 Dihedral angle restraints: 19064 sinusoidal: 7602 harmonic: 11462 Sorted by residual: dihedral pdb=" N PRO D 629 " pdb=" CG PRO D 629 " pdb=" CD PRO D 629 " pdb=" CB PRO D 629 " ideal model delta sinusoidal sigma weight residual 30.00 78.14 -48.14 1 1.50e+01 4.44e-03 1.42e+01 dihedral pdb=" CA PHE G 566 " pdb=" C PHE G 566 " pdb=" N ASN G 567 " pdb=" CA ASN G 567 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP C 717 " pdb=" CB ASP C 717 " pdb=" CG ASP C 717 " pdb=" OD1 ASP C 717 " ideal model delta sinusoidal sigma weight residual -30.00 -88.54 58.54 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 19061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4173 0.069 - 0.138: 583 0.138 - 0.207: 10 0.207 - 0.276: 1 0.276 - 0.345: 1 Chirality restraints: 4768 Sorted by residual: chirality pdb=" CA SER C 719 " pdb=" N SER C 719 " pdb=" C SER C 719 " pdb=" CB SER C 719 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA ASN C 720 " pdb=" N ASN C 720 " pdb=" C ASN C 720 " pdb=" CB ASN C 720 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE G 285 " pdb=" N ILE G 285 " pdb=" C ILE G 285 " pdb=" CB ILE G 285 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4765 not shown) Planarity restraints: 5509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 716 " 0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C LYS E 716 " -0.087 2.00e-02 2.50e+03 pdb=" O LYS E 716 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP E 717 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 664 " 0.060 5.00e-02 4.00e+02 8.89e-02 1.27e+01 pdb=" N PRO B 665 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 658 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO A 659 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 659 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 659 " -0.042 5.00e-02 4.00e+02 ... (remaining 5506 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 800 2.68 - 3.24: 28887 3.24 - 3.79: 45579 3.79 - 4.35: 64653 4.35 - 4.90: 107582 Nonbonded interactions: 247501 Sorted by model distance: nonbonded pdb=" OG SER H 34 " pdb=" OE2 GLU H 75 " model vdw 2.131 2.440 nonbonded pdb=" OG SER D 516 " pdb=" OD1 ASN D 610 " model vdw 2.182 2.440 nonbonded pdb=" OD2 ASP H 138 " pdb=" OG SER H 176 " model vdw 2.190 2.440 nonbonded pdb=" OG1 THR C 521 " pdb=" O GLU C 524 " model vdw 2.193 2.440 nonbonded pdb=" NH2 ARG B 394 " pdb=" O LEU B 444 " model vdw 2.197 2.520 ... (remaining 247496 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'B' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'C' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'D' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'E' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'F' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) selection = (chain 'G' and (resid 217 through 313 or resid 315 through 477 or resid 498 thro \ ugh 742 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.760 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 88.450 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.483 31261 Z= 0.232 Angle : 0.581 27.183 42364 Z= 0.338 Chirality : 0.045 0.345 4768 Planarity : 0.004 0.089 5509 Dihedral : 14.171 89.824 11726 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.75 % Allowed : 0.84 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3891 helix: 0.87 (0.22), residues: 588 sheet: 0.72 (0.16), residues: 1176 loop : -1.02 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 632 HIS 0.002 0.000 AHIS A 314 PHE 0.025 0.001 PHE D 707 TYR 0.025 0.001 TYR D 709 ARG 0.004 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 3.152 Fit side-chains revert: symmetry clash REVERT: C 716 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7346 (ttmt) REVERT: H 4 GLU cc_start: 0.5654 (tp30) cc_final: 0.5376 (tp30) REVERT: H 223 TRP cc_start: 0.8196 (t60) cc_final: 0.7881 (t60) REVERT: H 292 THR cc_start: 0.8467 (m) cc_final: 0.8008 (p) outliers start: 15 outliers final: 7 residues processed: 141 average time/residue: 0.4041 time to fit residues: 95.2263 Evaluate side-chains 107 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 300 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN H 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31261 Z= 0.288 Angle : 0.520 9.637 42364 Z= 0.278 Chirality : 0.045 0.174 4768 Planarity : 0.004 0.060 5509 Dihedral : 4.694 59.341 4221 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.86 % Allowed : 4.75 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3891 helix: 0.86 (0.22), residues: 594 sheet: 0.61 (0.15), residues: 1217 loop : -1.08 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 223 HIS 0.003 0.001 AHIS A 314 PHE 0.017 0.001 PHE G 707 TYR 0.017 0.001 TYR E 674 ARG 0.005 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 3.692 Fit side-chains revert: symmetry clash REVERT: C 654 THR cc_start: 0.5858 (p) cc_final: 0.5514 (p) REVERT: C 716 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7147 (ttpt) REVERT: D 668 ARG cc_start: 0.5660 (mmt180) cc_final: 0.5406 (ttm-80) REVERT: E 736 LEU cc_start: 0.8174 (mm) cc_final: 0.7942 (mm) REVERT: H 4 GLU cc_start: 0.5628 (tp30) cc_final: 0.5402 (tp30) REVERT: H 54 GLN cc_start: 0.7621 (mt0) cc_final: 0.7350 (mt0) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.4594 time to fit residues: 96.5928 Evaluate side-chains 120 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 688 ILE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 237 optimal weight: 0.0050 chunk 96 optimal weight: 5.9990 chunk 349 optimal weight: 10.0000 chunk 377 optimal weight: 0.3980 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 overall best weight: 2.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN F 431 ASN H 127 GLN H 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 31261 Z= 0.336 Angle : 0.538 10.858 42364 Z= 0.287 Chirality : 0.046 0.175 4768 Planarity : 0.004 0.057 5509 Dihedral : 4.716 44.802 4221 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.04 % Allowed : 7.03 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3891 helix: 0.75 (0.22), residues: 595 sheet: 0.58 (0.15), residues: 1187 loop : -1.21 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 223 HIS 0.003 0.001 AHIS A 314 PHE 0.016 0.002 PHE F 707 TYR 0.015 0.001 TYR E 674 ARG 0.004 0.000 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 3.756 Fit side-chains revert: symmetry clash REVERT: B 668 ARG cc_start: 0.5904 (tpm170) cc_final: 0.5644 (tpp-160) REVERT: C 691 LYS cc_start: 0.6714 (tttt) cc_final: 0.6458 (ttmt) REVERT: C 716 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7099 (ttpt) REVERT: D 668 ARG cc_start: 0.5842 (mmt180) cc_final: 0.5166 (ttm-80) REVERT: E 736 LEU cc_start: 0.8234 (mm) cc_final: 0.7946 (mm) REVERT: F 381 ILE cc_start: 0.8004 (tp) cc_final: 0.7703 (tt) REVERT: H 54 GLN cc_start: 0.7632 (mt0) cc_final: 0.7324 (mt0) outliers start: 24 outliers final: 16 residues processed: 130 average time/residue: 0.4137 time to fit residues: 91.5317 Evaluate side-chains 119 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 688 ILE Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 10.0000 chunk 262 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 0.3980 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 4.9990 chunk 371 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN F 431 ASN H 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31261 Z= 0.229 Angle : 0.483 9.642 42364 Z= 0.258 Chirality : 0.044 0.165 4768 Planarity : 0.003 0.056 5509 Dihedral : 4.446 40.051 4221 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.15 % Allowed : 8.18 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 3891 helix: 0.90 (0.22), residues: 596 sheet: 0.64 (0.16), residues: 1182 loop : -1.17 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 223 HIS 0.002 0.001 AHIS A 314 PHE 0.016 0.001 PHE F 707 TYR 0.011 0.001 TYR E 674 ARG 0.003 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 3.564 Fit side-chains revert: symmetry clash REVERT: B 668 ARG cc_start: 0.6051 (tpm170) cc_final: 0.5799 (tpm170) REVERT: C 691 LYS cc_start: 0.6703 (tttt) cc_final: 0.6454 (ttmt) REVERT: C 716 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7246 (ttpt) REVERT: D 639 ASN cc_start: 0.6856 (OUTLIER) cc_final: 0.6418 (p0) REVERT: D 668 ARG cc_start: 0.5798 (mmt180) cc_final: 0.5131 (ttm-80) REVERT: E 736 LEU cc_start: 0.8229 (mm) cc_final: 0.7920 (mm) REVERT: F 381 ILE cc_start: 0.8009 (tp) cc_final: 0.7696 (tt) REVERT: H 54 GLN cc_start: 0.7641 (mt0) cc_final: 0.7359 (mt0) outliers start: 27 outliers final: 19 residues processed: 132 average time/residue: 0.4107 time to fit residues: 91.2088 Evaluate side-chains 121 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 0.0980 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 189 optimal weight: 0.8980 chunk 333 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31261 Z= 0.182 Angle : 0.459 9.845 42364 Z= 0.244 Chirality : 0.044 0.164 4768 Planarity : 0.003 0.053 5509 Dihedral : 4.218 32.936 4221 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.24 % Allowed : 9.19 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3891 helix: 1.02 (0.22), residues: 602 sheet: 0.73 (0.16), residues: 1187 loop : -1.12 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 223 HIS 0.002 0.000 AHIS A 314 PHE 0.014 0.001 PHE F 707 TYR 0.020 0.001 TYR C 396 ARG 0.003 0.000 ARG A 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 5.100 Fit side-chains revert: symmetry clash REVERT: B 668 ARG cc_start: 0.6063 (tpm170) cc_final: 0.5839 (tpm170) REVERT: B 707 PHE cc_start: 0.6275 (p90) cc_final: 0.5853 (p90) REVERT: C 691 LYS cc_start: 0.6709 (tttt) cc_final: 0.6450 (ttmt) REVERT: C 716 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7390 (ttpt) REVERT: D 668 ARG cc_start: 0.5664 (mmt180) cc_final: 0.5376 (ttm-80) REVERT: E 736 LEU cc_start: 0.8191 (mm) cc_final: 0.7893 (mm) REVERT: H 54 GLN cc_start: 0.7642 (mt0) cc_final: 0.7354 (mt0) REVERT: H 223 TRP cc_start: 0.7457 (t-100) cc_final: 0.7071 (t60) outliers start: 29 outliers final: 20 residues processed: 137 average time/residue: 0.4003 time to fit residues: 93.9442 Evaluate side-chains 123 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 4.9990 chunk 334 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 371 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 627 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31261 Z= 0.162 Angle : 0.447 9.421 42364 Z= 0.238 Chirality : 0.043 0.161 4768 Planarity : 0.003 0.050 5509 Dihedral : 4.077 33.076 4221 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.18 % Allowed : 9.71 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3891 helix: 1.14 (0.22), residues: 602 sheet: 0.81 (0.16), residues: 1186 loop : -1.05 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 223 HIS 0.001 0.000 AHIS A 314 PHE 0.013 0.001 PHE F 707 TYR 0.010 0.001 TYR D 261 ARG 0.003 0.000 ARG H 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 3.990 Fit side-chains revert: symmetry clash REVERT: B 707 PHE cc_start: 0.6187 (p90) cc_final: 0.5698 (p90) REVERT: C 691 LYS cc_start: 0.6686 (tttt) cc_final: 0.6426 (ttmt) REVERT: D 639 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6427 (p0) REVERT: D 668 ARG cc_start: 0.5657 (mmt180) cc_final: 0.5359 (ttm-80) REVERT: E 736 LEU cc_start: 0.8166 (mm) cc_final: 0.7884 (mm) REVERT: H 54 GLN cc_start: 0.7617 (mt0) cc_final: 0.7321 (mt0) outliers start: 27 outliers final: 23 residues processed: 128 average time/residue: 0.4091 time to fit residues: 89.3066 Evaluate side-chains 127 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain E residue 720 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 634 ASN Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 312 optimal weight: 0.0070 chunk 207 optimal weight: 9.9990 chunk 370 optimal weight: 8.9990 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 0.0870 chunk 170 optimal weight: 0.9980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 627 ASN F 523 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31261 Z= 0.110 Angle : 0.422 10.738 42364 Z= 0.224 Chirality : 0.042 0.158 4768 Planarity : 0.003 0.051 5509 Dihedral : 3.748 32.820 4221 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.21 % Allowed : 10.02 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3891 helix: 1.34 (0.23), residues: 595 sheet: 0.94 (0.16), residues: 1155 loop : -0.89 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 223 HIS 0.001 0.000 HIS H 157 PHE 0.015 0.001 PHE B 711 TYR 0.010 0.001 TYR F 396 ARG 0.007 0.000 ARG B 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 3.771 Fit side-chains revert: symmetry clash REVERT: B 707 PHE cc_start: 0.6021 (p90) cc_final: 0.5708 (p90) REVERT: C 691 LYS cc_start: 0.6664 (tttt) cc_final: 0.6379 (ttmt) REVERT: C 716 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7612 (tmtt) REVERT: D 639 ASN cc_start: 0.6675 (OUTLIER) cc_final: 0.5968 (p0) REVERT: D 668 ARG cc_start: 0.5502 (mmt180) cc_final: 0.5069 (ttm-80) REVERT: E 736 LEU cc_start: 0.8108 (mm) cc_final: 0.7844 (mm) REVERT: H 54 GLN cc_start: 0.7582 (mt0) cc_final: 0.7357 (mt0) REVERT: H 223 TRP cc_start: 0.7645 (t-100) cc_final: 0.7190 (t60) REVERT: H 292 THR cc_start: 0.8415 (m) cc_final: 0.7939 (p) outliers start: 28 outliers final: 17 residues processed: 143 average time/residue: 0.4170 time to fit residues: 100.1907 Evaluate side-chains 129 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 660 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 411 ASN C 225 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN F 431 ASN F 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 31261 Z= 0.343 Angle : 0.521 9.790 42364 Z= 0.277 Chirality : 0.045 0.170 4768 Planarity : 0.003 0.051 5509 Dihedral : 4.305 33.975 4221 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.18 % Allowed : 10.40 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3891 helix: 1.05 (0.22), residues: 602 sheet: 0.74 (0.16), residues: 1199 loop : -1.06 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 223 HIS 0.003 0.001 AHIS A 314 PHE 0.015 0.001 PHE G 707 TYR 0.015 0.001 TYR H 183 ARG 0.005 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 3.510 Fit side-chains REVERT: B 707 PHE cc_start: 0.6270 (p90) cc_final: 0.5797 (p90) REVERT: C 691 LYS cc_start: 0.6689 (tttt) cc_final: 0.6401 (ttmt) REVERT: D 639 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6364 (p0) REVERT: D 668 ARG cc_start: 0.5825 (mmt180) cc_final: 0.5515 (ttm-80) REVERT: E 736 LEU cc_start: 0.8192 (mm) cc_final: 0.7883 (mm) REVERT: H 54 GLN cc_start: 0.7618 (mt0) cc_final: 0.7397 (mt0) outliers start: 26 outliers final: 22 residues processed: 124 average time/residue: 0.4031 time to fit residues: 84.7351 Evaluate side-chains 121 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 660 MET Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 chunk 323 optimal weight: 0.8980 chunk 344 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 343 optimal weight: 0.0170 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 627 ASN F 431 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31261 Z= 0.200 Angle : 0.469 10.340 42364 Z= 0.250 Chirality : 0.044 0.158 4768 Planarity : 0.003 0.051 5509 Dihedral : 4.158 32.735 4221 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.21 % Allowed : 10.34 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3891 helix: 1.10 (0.22), residues: 602 sheet: 0.85 (0.16), residues: 1151 loop : -1.03 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 223 HIS 0.002 0.001 AHIS A 314 PHE 0.013 0.001 PHE F 707 TYR 0.011 0.001 TYR B 396 ARG 0.004 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 3.122 Fit side-chains REVERT: A 720 ASN cc_start: 0.6648 (m-40) cc_final: 0.6374 (m110) REVERT: B 707 PHE cc_start: 0.6252 (p90) cc_final: 0.5778 (p90) REVERT: C 691 LYS cc_start: 0.6666 (tttt) cc_final: 0.6377 (ttmt) REVERT: D 639 ASN cc_start: 0.6783 (OUTLIER) cc_final: 0.6376 (p0) REVERT: D 668 ARG cc_start: 0.5757 (mmt180) cc_final: 0.5425 (ttm-80) REVERT: E 736 LEU cc_start: 0.8160 (mm) cc_final: 0.7863 (mm) REVERT: H 54 GLN cc_start: 0.7578 (mt0) cc_final: 0.7275 (mt0) outliers start: 27 outliers final: 25 residues processed: 120 average time/residue: 0.3904 time to fit residues: 78.8546 Evaluate side-chains 127 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain E residue 688 ILE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 660 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 582 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 2.9990 chunk 364 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 253 optimal weight: 0.6980 chunk 382 optimal weight: 7.9990 chunk 352 optimal weight: 0.9990 chunk 304 optimal weight: 7.9990 chunk 31 optimal weight: 0.0770 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 627 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31261 Z= 0.118 Angle : 0.429 9.618 42364 Z= 0.228 Chirality : 0.043 0.161 4768 Planarity : 0.003 0.050 5509 Dihedral : 3.793 30.706 4221 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.04 % Allowed : 10.57 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3891 helix: 1.33 (0.22), residues: 595 sheet: 1.04 (0.16), residues: 1143 loop : -0.89 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 223 HIS 0.001 0.000 HIS H 157 PHE 0.011 0.001 PHE F 707 TYR 0.012 0.001 TYR B 396 ARG 0.004 0.000 ARG F 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 3.601 Fit side-chains REVERT: B 707 PHE cc_start: 0.5972 (p90) cc_final: 0.5501 (p90) REVERT: C 691 LYS cc_start: 0.6766 (tttt) cc_final: 0.6505 (ttmt) REVERT: C 716 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7719 (tptp) REVERT: D 639 ASN cc_start: 0.6675 (OUTLIER) cc_final: 0.6089 (p0) REVERT: D 668 ARG cc_start: 0.5547 (mmt180) cc_final: 0.5092 (ttm-80) REVERT: E 736 LEU cc_start: 0.8104 (mm) cc_final: 0.7835 (mm) REVERT: H 54 GLN cc_start: 0.7531 (mt0) cc_final: 0.7260 (mt0) outliers start: 21 outliers final: 19 residues processed: 129 average time/residue: 0.4233 time to fit residues: 91.7334 Evaluate side-chains 125 residues out of total 3407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 594 THR Chi-restraints excluded: chain C residue 716 LYS Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 639 ASN Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 523 ASN Chi-restraints excluded: chain E residue 657 LYS Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 660 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.5980 chunk 324 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 127 optimal weight: 0.3980 chunk 313 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 627 ASN F 425 GLN H 318 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.106460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070541 restraints weight = 202799.932| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.07 r_work: 0.2977 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31261 Z= 0.120 Angle : 0.428 10.492 42364 Z= 0.227 Chirality : 0.042 0.164 4768 Planarity : 0.003 0.049 5509 Dihedral : 3.709 29.677 4221 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.09 % Allowed : 10.71 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3891 helix: 1.40 (0.22), residues: 595 sheet: 1.15 (0.16), residues: 1143 loop : -0.84 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 223 HIS 0.001 0.000 AHIS A 314 PHE 0.011 0.001 PHE F 707 TYR 0.012 0.001 TYR B 396 ARG 0.004 0.000 ARG F 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5705.73 seconds wall clock time: 110 minutes 10.76 seconds (6610.76 seconds total)